14 #include "../exception/exceptionnotfound.h"
15 #include "../exception/exceptionnotpossible.h"
17 #include "../msrun/msrunid.h"
18 #include "../msrun/private/pwizmsrunreader.h"
19 #include "../msrun/private/timsmsrunreader.h"
20 #include "../msrun/private/timsmsrunreaderms2.h"
21 #include "../msrun/xymsrunreader.h"
29 const QString &xml_prefix)
30 : m_fileName(file_name), m_xmlPrefix(xml_prefix)
32 QFile file(file_name);
35 .arg(QFileInfo(file_name).absoluteFilePath())));
40 : m_fileName(other.m_fileName),
41 m_xmlPrefix(other.m_xmlPrefix),
42 m_fileFormat(other.m_fileFormat),
43 m_fileReaderType(other.m_fileReaderType)
66 std::vector<MsRunIdCstSPtr>
75 std::vector<MsRunIdCstSPtr> ms_run_ids =
92 if(!QFileInfo(tims_dir).isDir())
94 tims_dir = QFileInfo(
m_fileName).absolutePath();
101 if(ms_run_ids.size())
126 if(ms_run_ids.size())
148 if(!QFileInfo(tims_dir).isDir())
150 tims_dir = QFileInfo(
m_fileName).absolutePath();
154 std::vector<MsRunIdCstSPtr> ms_run_ids =
157 if(ms_run_ids.size())
164 return std::make_shared<TimsMsRunReaderMs2>(ms_run_ids.front());
169 QObject::tr(
"Unable to read mz data directory %1 with TimsTOF reader.")
179 QObject::tr(
"The MsRunId instance must have the name file name as the "
180 "MsFileAccessor.")));
184 qDebug() <<
"Returning a PwizMsRunReader.";
186 return std::make_shared<PwizMsRunReader>(ms_run_id);
190 qDebug() <<
"Returning a XyMsRunReader.";
192 return std::make_shared<XyMsRunReader>(ms_run_id);
197 qDebug() <<
"Returning a TimsMsRunReader.";
199 return std::make_shared<TimsMsRunReader>(ms_run_id);
203 qDebug() <<
"Returning a TimsMsRunReaderMs2.";
205 return std::make_shared<TimsMsRunReaderMs2>(ms_run_id);
212 return std::make_shared<XyMsRunReader>(ms_run_id);
216 return std::make_shared<PwizMsRunReader>(ms_run_id);
234 QFile file(ms_run_id.get()->getFileName());
237 QObject::tr(
"unable to build a reader : file %1 not found.")
238 .arg(QFileInfo(ms_run_id.get()->getFileName()).absoluteFilePath())));
240 MzFormat file_format = ms_run_id.get()->getMzFormat();
244 qDebug() <<
"Returning a XyMsRunReader.";
246 return std::make_shared<XyMsRunReader>(ms_run_id);
251 QObject::tr(
"unable to build a reader for %1 : unknown file format")
252 .arg(QFileInfo(ms_run_id.get()->getFileName()).absoluteFilePath())));
258 return std::make_shared<TimsMsRunReader>(ms_run_id);
263 return std::make_shared<TimsMsRunReaderMs2>(ms_run_id);
266 qDebug() <<
"by default, build a TimsMsRunReader.";
267 return std::make_shared<TimsMsRunReader>(ms_run_id);
271 qDebug() <<
"Returning a PwizMsRunReader .";
273 return std::make_shared<PwizMsRunReader>(ms_run_id);
279 const QString &xml_id)
281 qDebug() <<
"GGGGGGGGG1";
282 std::vector<MsRunIdCstSPtr> run_list =
getMsRunIds();
284 qDebug() <<
"GGGGGGGGG";
287 if(original_run_id.get()->getRunId() == run_id)
289 MsRunId new_run_id(*original_run_id.get());
296 if((run_id.isEmpty()) && (run_list.size() == 1))
298 MsRunId new_run_id(*run_list[0].get());
305 if(reader_sp ==
nullptr)
310 .arg(QFileInfo(
m_fileName).absoluteFilePath())));
320 std::pair<MzFormat, FileReaderType>(format, reader_type));
324 ret.first->second = reader_type;
MzFormat getFileFormat() const
get the raw format of mz data
MsRunReaderSPtr msRunReaderSp(MsRunIdCstSPtr ms_run_id)
const QString m_xmlPrefix
void setPreferedFileReaderType(MzFormat format, FileReaderType reader_type)
given an mz format, explicitly set the prefered reader
virtual ~MsFileAccessor()
FileReaderType getFileReaderType() const
get the file reader type
std::map< MzFormat, FileReaderType > m_preferedFileReaderTypeMap
std::vector< MsRunIdCstSPtr > getMsRunIds()
FileReaderType m_fileReaderType
MsRunReaderSPtr getMsRunReaderSPtrByRunId(const QString &run_id, const QString &xml_id)
get an msrun reader by finding the run_id in file
MsFileAccessor(const QString &file_name, const QString &xml_prefix)
static MsRunReaderSPtr buildMsRunReaderSPtr(MsRunIdCstSPtr ms_run_id)
get an MsRunReader directly from a valid MsRun ID
TimsMsRunReaderMs2SPtr buildTimsMsRunReaderMs2SPtr()
if possible, builds directly a dedicated Tims TOF tdf file reader
const QString & getFileName() const
MS run identity MsRunId identifies an MS run with a unique ID (XmlId) and contains eventually informa...
void setXmlId(const QString &xml_id)
set an XML unique identifier for this MsRunId
virtual std::vector< MsRunIdCstSPtr > getMsRunIds(const QString &run_prefix) override
virtual MzFormat getFileFormat() override
virtual std::vector< MsRunIdCstSPtr > getMsRunIds(const QString &run_prefix) override
virtual MzFormat getFileFormat() override
virtual std::vector< MsRunIdCstSPtr > getMsRunIds(const QString &run_prefix) override
virtual MzFormat getFileFormat() override
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
std::shared_ptr< MsRunReader > MsRunReaderSPtr
std::shared_ptr< TimsMsRunReaderMs2 > TimsMsRunReaderMs2SPtr
std::shared_ptr< const MsRunId > MsRunIdCstSPtr
MSrun file reader for native Bruker TimsTOF raw data.